Data-driven modelling of biological multi-scale processes

Biological processes involve a variety of spatial and temporal scales. A holistic understanding of many biological processes therefore requires multi-scale models which capture the relevant properties on all these scales. In this manuscript we review mathematical modelling approaches used to describe the individual spatial scales and how they are integrated into holistic models. We discuss the relation between spatial and temporal scales and the implication of that on multi-scale modelling. Based upon this overview over state-of-the-art modelling approaches, we formulate key challenges in mathematical and computational modelling of biological multi-scale and multi-physics processes. In particular, we considered the availability of analysis tools for multi-scale models and model-based multi-scale data integration. We provide a compact review of methods for model-based data integration and model-based hypothesis testing. Furthermore, novel approaches and recent trends are discussed, including computation time reduction using reduced order and surrogate models, which contribute to the solution of inference problems. We conclude the manuscript by providing a few ideas for the development of tailored multi-scale inference methods.Comment: This manuscript will appear in the Journal of Coupled Systems and Multiscale Dynamics (American Scientific Publishers

Distributed Hybrid Simulation of the Internet of Things and Smart Territories

This paper deals with the use of hybrid simulation to build and compose heterogeneous simulation scenarios that can be proficiently exploited to model and represent the Internet of Things (IoT). Hybrid simulation is a methodology that combines multiple modalities of modeling/simulation. Complex scenarios are decomposed into simpler ones, each one being simulated through a specific simulation strategy. All these simulation building blocks are then synchronized and coordinated. This simulation methodology is an ideal one to represent IoT setups, which are usually very demanding, due to the heterogeneity of possible scenarios arising from the massive deployment of an enormous amount of sensors and devices. We present a use case concerned with the distributed simulation of smart territories, a novel view of decentralized geographical spaces that, thanks to the use of IoT, builds ICT services to manage resources in a way that is sustainable and not harmful to the environment. Three different simulation models are combined together, namely, an adaptive agent-based parallel and distributed simulator, an OMNeT++ based discrete event simulator and a script-language simulator based on MATLAB. Results from a performance analysis confirm the viability of using hybrid simulation to model complex IoT scenarios.Comment: arXiv admin note: substantial text overlap with arXiv:1605.0487

Digital Ecosystems: Ecosystem-Oriented Architectures

We view Digital Ecosystems to be the digital counterparts of biological ecosystems. Here, we are concerned with the creation of these Digital Ecosystems, exploiting the self-organising properties of biological ecosystems to evolve high-level software applications. Therefore, we created the Digital Ecosystem, a novel optimisation technique inspired by biological ecosystems, where the optimisation works at two levels: a first optimisation, migration of agents which are distributed in a decentralised peer-to-peer network, operating continuously in time; this process feeds a second optimisation based on evolutionary computing that operates locally on single peers and is aimed at finding solutions to satisfy locally relevant constraints. The Digital Ecosystem was then measured experimentally through simulations, with measures originating from theoretical ecology, evaluating its likeness to biological ecosystems. This included its responsiveness to requests for applications from the user base, as a measure of the ecological succession (ecosystem maturity). Overall, we have advanced the understanding of Digital Ecosystems, creating Ecosystem-Oriented Architectures where the word ecosystem is more than just a metaphor.Comment: 39 pages, 26 figures, journa